Implementation of sMRI pipeline: AVOID passing on skull-stripped output from cat12

[finnlennartsson]

Axel's pipeline is a replica of the Knapen Lab's anatomical workflows.

There is an important difference though. In the original pipeline, the output should be a denoised T1w image (both background and internal noise removal). Axel's pipeline is outputting a denoised but skull-stripped T1w image.

The recommendation from fMRIprep is not to use a skull-stripped image. See point in FAQ and relevant neurostars issues related to this (see links in FAQ entry).

[emilljungberg]

This has been updated now in 7b0829e. The cat12 command now runs as it should but the output files stays in the cat12 folder. Todo:

1. Move files to raw data
   .../cat12/sub-XXX_desc-pymp2ragecat12_T1w.nii.gz
   to
   raw data/sub<X>/anat/sub-XXX_rec-pymp2rageCat12_UNIT1.nii.gz
   Note how we have swapped from desc to rec which stands for reconstruction.

2. Copy over the corresponding .json sidecar.

3. This new file must be added into studydir/rawdata/sub-XXX/sub-XXX_scans.tsv.

[emilljungberg]

This has now been completed with 6ceef5d. Axel has implemented that the new file gets copied to rawdata/sub<X>/anat/sub-XXX_rec-pymp2rageCat12_UNIT1.nii.gz. The json sidecar is also included and the new file is added to the scans.tsv file.